Managed to solve the problem with much hair-pulling. For some reason (perhaps platform dependant), perl (or probably more correctly passwd itself) refuses to accept a change of password when run
system "/usr/bin/passwd", $username;
I am happy enough leaving this fact alone, and have rather manually taken in the passwd and encrypted it with crypt. This is probably superfluous, but I may as well show you what I did in case someone has this problem in the future.
print "Password: ";
chomp(my $passwd = <STDIN>);
$passwd = crypt($passwd, time());
$uid=($max+1);
system '/usr/sbin/useradd', "-u $uid", '-s', $shell,
'-p', $passwd, '-g 100', '-m', $username;
So simple in hindsight. Perl really humbles me!
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